The Sosnick Group at The University of Chicago


The Sosnick Group strives to characterize the general principles that guide protein folding and dynamics. We combine multiple experimental and computational approaches to characterize the behavior of proteins in diverse contexts


Positions available!

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SAXS analysis - collapsed or expanded

Given small angle X-ray scattering (SAXS) dataset for an intrinsically disordered protein (IDP), we have developed an analysis method that can determine both the dimension of the ensemble as well as the quality of the solvent (i.e. the extent of self-interactions in the IDP).

Protein Folding - the 70% Rule

We have found that for many small 2-state proteins, the rate-limiting step of folding - the transition state - has ~70% of the native topology, according to the relative contact order.

 

Molecular Dynamics on your laptop!

Wouldn't it be nice to have physically realistic MD trajectories of protein dynamics without needing cpu-weeks/months of simulations? We have developed an MD engine that can reversibly fold some proteins up to 97 amino acids in cpu-days without requiring the use of fragments, homology or evolution.

Paper Published 01/02/2019

John JumperNabil Faruk

Congratulations to John Jumper and Nabil Faruk on having their recent paper, "Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours", published in PLoS Computational Biology.

Paper Published 01/02/2019

John JumperNabil Faruk

Congratulations to John Jumper and Nabil Faruk on having their recent paper,"Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics", published in PLoS Computational Biology.

Paper Published 11/14/2018

Zongan WangJohn Jumper

Congratulations to Zongan Wang, John Jumper and Sheng Wang on having their recent paper published in Biophysical Journal, entitled "A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations". Upside has now been applied to membrane proteins!

Welcome 09/24/2018

Xiangda Peng

Welcome to Xiangda Peng, who is joining us as a Postdoctoral Scholar!

Protein Folding

Protein Folding

Predicting Folding Dynamics

Predicting Folding Dynamics

Photoswitchable allosteric proteins

Photoswitchable allosteric proteins

Membrane Proteins

Membrane Proteins

Psi analysis

Psi analysis

Conformational Entropy

Conformational Entropy

J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics" PLoS Comput Biol 14(12: e1006342

J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours" PLoS Comput Biol. 14(12): e1006578

Z. Wang, J.M. Jumper, S. Wang, K.F. Freed, T.R. Sosnick, "A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations." Biophysical Journal, 115 (2018) 1872-84.

J.R. Riback, M.A. Bowman, A.M. Zmyslowski, C.R. Knoverek, J.M. Jumper, E.B. Haye, K.F. Freed, P.L. Clark, T.R. Sosnick, "Response to Comment on 'Innovative scattering analysis shows hydrophobic disordered proteins are expanded in water'" Science 361 (2018).

J.A. Riback, M.A. Bowman, A.M. Zmyslowski, K.W. Plaxco, P.L. Clark, T.R. Sosnick, "Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein." bioRxiv:376632.

J.J. Skinner, S. Wang, J. Lee, C. Ong, R. Sommese, S. Sivaramakrishnan, W. Koelmel, M. Hirschbeck, H. Schindelin, C. Kisker, K. Lorenz, T.R. Sosnick, M.R. Rosner, "Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome." Proc Natl Acad Sci U S A 114 (2017) 13453-8.

University of Chicago
Biochemistry & Molecular Biophsyics
Biophysical Sciences
Institute for Molecular Engineering
Institute for Biophysical Dynamics